Apologies if this question has been asked and answered before/has a ridiculously obvious answer.

Basically I'm working in After Effects CS6 and I'm rotoscoping a 50 second sequence (a girl walking down some stairs in a floaty dress), the process is taking me a while do to the movement of her dress and so I was wondering if there is any way that I can save the project mod rotoscoping in order to return to it later without losing my progress with the rotoscoping I've already done.

There's nothing to do. You just save the project. AE retains the Rotobrush data and things like masks are just parametric boundary definitions, anyway. You are overthinking this. The only caveat is that it may take a long time to run through the RB analysis again when re-opening the project. Thus, depending on what progress you already have made, you might consider just rendering out an intermediate clip with transparency and using that later.